GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lat in Bacteroides thetaiotaomicron VPI-5482

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)

Query= reanno::Pedo557:CA265_RS14455
         (443 letters)



>lcl|FitnessBrowser__Btheta:353284 BT3758 acetylornithine
           aminotransferase (NCBI ptt file)
          Length = 373

 Score =  154 bits (389), Expect = 5e-42
 Identities = 128/426 (30%), Positives = 203/426 (47%), Gaps = 75/426 (17%)

Query: 28  YDME--KSHGAYIYDAKHNRTLLDFFTCFASVPLGYNHP---KMINDEAFKKNLFLAALA 82
           YD+   K  G  ++D ++    LD +   A + +G+ HP   +MI+++       +A L 
Sbjct: 10  YDINIVKGQGCKVWD-ENGTEYLDLYGGHAVISIGHAHPHYVEMISNQ-------VATLG 61

Query: 83  NPSNSDVYTQQYAQFVETFSKV-GIPDYLPHAFFIAGGGLAVENAIKVAMDWKVQKNFAK 141
             SNS V  +   Q  E   K+ G  DY    F I  G  A ENA+K+A       +F  
Sbjct: 62  FYSNS-VINKLQQQVAERLGKISGYEDY--SLFLINSGAEANENALKLA-------SFYN 111

Query: 142 GYTEEKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNL 201
           G T     KV+ F +AFHGRT   +  TN                   P +  P+  NN 
Sbjct: 112 GRT-----KVISFSKAFHGRTSLAVEATNN------------------PTIIAPI--NNN 146

Query: 202 SHAIQTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAF 261
            H        +  +K+ +A  K D+CA+I+E IQ  GG      EF+ +++ +  E    
Sbjct: 147 GHVTYLPLNDIEAMKQELA--KGDVCAVIIEGIQGVGGIKIPTTEFMQELRKVCTETGTI 204

Query: 262 LIYDEVQTGVGLTGKFWCHQHFSEKARPDIL----AFGKKMQVCGILVGHKVDQVETNVF 317
           LI DE+Q+G G +GKF+ HQ+     +PDI+      G    + G+L+        + +F
Sbjct: 205 LILDEIQSGYGRSGKFFAHQY--NHIQPDIITVAKGIGNGFPMAGVLI--------SPMF 254

Query: 318 K-VPSRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYLKDQLENLSHRFDQMTN 376
           K V  ++ +T+GGN +    +  ++ ++E+D L ENA  VG YL ++L+    +F Q+  
Sbjct: 255 KPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLEELK----KFPQIKE 310

Query: 377 VRGRGLLCSFDF--PTKEMRNTFIAKGLENNVMFLGCGEKTIRFRPALCIEQKHIDEGLT 434
           VRGRGL+   +F  P KE+R+  I    + +V     G   +R  P LC+  +  DE L 
Sbjct: 311 VRGRGLMIGLEFEEPIKELRSRLI---YDEHVFTGASGTNVLRLLPPLCLSMEEADEFLA 367

Query: 435 VMDKIL 440
              ++L
Sbjct: 368 RFKRVL 373


Lambda     K      H
   0.321    0.137    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 405
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 443
Length of database: 373
Length adjustment: 31
Effective length of query: 412
Effective length of database: 342
Effective search space:   140904
Effective search space used:   140904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory